Question: Given a list of cell surface genes, is there a computational possibility to predict their interaction partners on the surface of another cell?
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gravatar for charlesgwellem
27 days ago by
charlesgwellem0 wrote:

Hi folks. After performing differential expression analyses on my single cell RNA sequencing data from ILC2s of mouse origin, treated under three conditions, I generated a list of differentially genes. I afterwards used the Gene Ontology platform to generate a shorter list of genes proven to be present on the surface of mouse cells. Is there a computational possibilty to predict interaction partners of these ILC2 surface genes present on the surface of mouse fibroblast cells?

Thank you in advance for your help.

ADD COMMENTlink modified 26 days ago by kristoffer.vittingseerup1.4k • written 27 days ago by charlesgwellem0

1)This is not exactly what you asked for, but I've found a pdf-file describing molecular docking

and a lot of tools to work with it. http://caps.ncbs.res.in/download/mmpli_talks/Softwares_for_Molecular_Docking.pdf

It's from 2007, some soft may not exist any more, but it's worth looking at, I think.

2)There is another article of virus-receptor binding, https://peerj.com/articles/266.pdf

It mentions some computational tools as well.

3) There is a large drug-design database.

Directory of computer-aided Drug Design tools:

http://www.click2drug.org/

4) Cell-surface human proteins, a post from biostars:

Database of human genes encoding cell surface proteins

ADD REPLYlink modified 26 days ago • written 26 days ago by natasha.sernova3.3k
3
gravatar for kristoffer.vittingseerup
26 days ago by
European Union
kristoffer.vittingseerup1.4k wrote:

I do not think so. The best approach I have seen was this paper whether they use a currated list of receptor-ligant interactions (available here) and tried using the expression of those pairs. But to my knowledge no computational tool.

ADD COMMENTlink written 26 days ago by kristoffer.vittingseerup1.4k
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